Phantom
by karkashan
Summary: The war is over, indoctrination wiped away by a green light. Yet all is not calm, and not everyone wants peace. Waking up months later, one amnesiac Phantom will have to decide where her loyalties lie, before it's all too late.
1. With His Nineteen Men So Few

_Darkness._

"I don't like this," said a helmeted soldier to another as they gazed at the Omega skyline.

"That's five times now, Jenkins," said the other, "and would you relax? Everything is still within the predetermined mission parameters."

"We're far too exposed here though, Roberts. And everyone on this rotten station is paranoid about us showing up again since General Oleg was ousted," said Jenkins, the crackling of voice modulation disguising any of the more subtle emotions he might have been feeling beneath his yellow visor.

_It is from that infinite void from which all of us spring; and in time, it is where we shall return._

"I have movement on the perimeter," a third voice called out.

Jenkins straightened his posture, the soft glow of his biotics coated his hands as he back away from the guard railing. "What do you see, Nikolic?.

"Please say Turians with a death wish, Sandra," said Roberts with the smallest hint of humor in his voice, "that would make my day complete."

_I have not yet been given to that endless expanse of darkness. But yet, I feel it in my mind._

"Negative, Harry," the female voice of Sandra Nikolic said to Roberts in reply, "looks like an Alliance special ops squad."

This caused Roberts to straighten his posture immediately. "Alliance? But they have no authority on Omega." He glanced up at the position the Nemesis infiltrator was no doubt looking though her scope, his incredulity in his expression shining through despite being covered up by his Engineer's helmet. "And running a black op here would more than likely be considered 'fucking with Aria', which is the last thing the System Alliance needs."

"Roberts?" asked Nikolic, "did I ask for a fucking dissertation about the potential political fallout that our enemies might find themselves in due to kicking our collective ass?"

"No ma'am."

"Then please shut the fuck up and get you annoying little turret into position, because I'm looking at N7 Destroyer armor; and between you, me, and our little dragon boy, I don't think he's wearing that because he wants to politely ask me out on a date."

"Timmy's not annoying!" "It's Dragoon, not Dragon, Sandra!" Both Roberts and Jenkins said simultaneously.

"Yeah, yeah, whatever. Now would someone just like to make sure Slicing Beauty is ready for pickup? Transport'll be here in 5."

_It is for that reason, that darkness inside of me, that these insects seek to protect me._

"Seriously, Roberts, Timmy?" asked a somewhat incredulous Jenkins as he activated his omni-tool. "What, are you gonna star in a children's extranet series called "Timmy the Turret and the Emancipated Engineer"?"

"Thanks for the tip," Roberts said sarcastically as he set down his portable turret, "but if you must know I call him Timmy in mock memory of our formerly alive but now exploded former, yet illustrious, leader."

Jenkins snorted softly, but the sound was still picked up by his helmet's comm. Tapping a few more of the buttons on the projected interface of his omni-tool, he the held it up to the stasis pod as he asked, "Still mad about the whole 'implanting indoctrination technology into all of our faces' thing, aren't you?"

"A little bit, yeah," the other man replied as the turret unfolded with a quirky 'now online' emanated from its tiny speaker. "Though I'm not sure if the Major's so-called 'visions' are all that great of a plan to follow, at least I have a choice about it this time."

"I wonder what Sandra's 'Slicing Princess' would choose?"

_I am a wellspring, a reservoir from which to draw. Through this, these humans are able to drink minute traces of what is offered._

"Maybe you can ask her once this new tech gets rid of the weird after-effects a lot of our Phantoms have been suffering ever since the Crucible firing. In the meantime," Roberts raised his arm almost lazily, before firing a single bullet from his M-5 Phalanx. His aim was true, and the Alliance tech drone dissolved into a mess of static almost instantaneously, "we've got company."

_But they do not fully comprehend. How can they? They are but rudimentary creatures. _

"Target acquired," said Jenkins simply as he leapt towards the location of a crouched Alliance operative. His biotic lash ripped through the atmospheric particles of the station before latching themselves on the soon to be helpless enemy combatant. Ripping her from cover and towards him, he lifted a foot up as if to stomp the life from her, when a distinctive _clink_ noise reached his auditory nerve.

_Though they are but dust struggling against cosmic winds, they will endure, adapt, evolve. An admirable, if foolhardy quality of their species._

_I feel my mind fumbling around in ignorance, incapable of understanding without prior knowledge of my own history._

"Grenade!" he shouted before running and diving for cover next to Roberts. The ensuing explosion knocked them both to the ground. Before they good get up, however, they were quickly surrounded by three armed Alliance troops; the Engineer from earlier, an N7 Destroyer, and a what looked to be a Project Phoenix ex-Cerberus operative. "Shit," was the only word he could muster.

_Wait, am I one of them? But a speck upon the cosmos, denying my destiny that is in my genes?_

"Commander, I've got the other one!" shouted what was undoubtedly the fourth member of the Alliance Special Ops squad. "You were right, she's a sniper."

_No. I am not. For the briefest of moments, I felt the glory of unity with the cosmos. I shared my consciousness with the collective that was my sisters and myself. I beheld my destiny._

"Clarkson," said the N7 Destroyer, no doubt in the Cerberus foot-soldiers' minds that he was the commander, "find out what that thing they were transporting was. I wanna know what one of the remaining Cerberus factions not aligned with that crazy-ass Colonel risked coming to Omega for."

_I, am Ascended, and none will stand in my way._

The briefest moment filled with the sound of screeching metal was all the time the Alliance operatives had before the metal hatch of the container was launched at the approaching Engineer. Taking advantage of the distraction, Jenkins used his biotics to launch the two male enemy soldiers over the side of the railing and onto the loading dock 80-some odd meters below.

A groan came from the now-open stasis pod, and a Phantom, if a more custom-tailored one, walked out on unsteady feet. She gripped one hand to her head, as if trying to rub away a headache, while the other gripped her blade in a vice-like grip. She finally noticed the two Cerberus operatives standing there, watching her, and took a shaky step forward. This however, might have been somewhat of a premature action, as her sense of balance was still a bit off.

Before she could fall, however, the last member of the Cerberus squad, the Nemesis Sandra, dropped down from above and moved quickly to support the stumbling biotic. "I've got you, princess, no need to rush."

"You saying I should get my face plastered on a cup along with Belle and Jasmine?" said the tired voice of the newly woken Phantom.

"Aw," Sandra said with a snicker, "I always knew you ninja girls had a sense of humor underneath all those ugly-ass microwaves baked into your faces; we just had to short-circuit the appliances first."

"Couldn't tell you for sure," the Phantom replied, "because joining my mind with every other Phantom has kinda fried my ability to remember much of anything."

"Shit," said Jenkins, "is that what happened to you gals when the Crucible fired?" At the Phantom's slight nod, he shook his head, "Imagine that must've been like being a part of Reaper must be like."

"I'm pretty sure that's exactly what was happening. The last thing I can remember was that I was going to 'stop anyone who stood in the way of my genetic destiny'."

"Let's let the lady rest for a few before grilling her on her experiences," said Sandra to the rest of her team, "Shuttle's here, and I don't want to keep the Major waiting too long."

* * *

"You sure about this intel, Commander?"

"Yes sir. Picked it up from one of Clarkson's bugs after the failure of the mission."

"Your mission was to give the Alliance new intel about the situation with a Cerberus remnant, Commander. You did that and more. I'm calling that a success. Hackett, out."

The image of the N7 marine flickered out, and a female voice spoke from behind Admiral Hackett. "He didn't capture the Cerberus team or the device they were transporting, and you're calling the mission a success? Just what kind of intel did he give you?"

"Admiral Shepard," Hackett acknowledged, the cybernetics that were now a part of him allowing him to make out her face in the dim light of the conference room. "If you must know, we just received intel, not only on one of the leaders of the Cerberus remnants, but also something even more important than that. We've got a recording of a Cerberus Phantom detailing her recollection of what happened after the Crucible fired."

Hannah Shepard's eyes widened, "I thought they went crazy if awoken, not able to talk in anything but gibberish and needing to be put in stasis due to their inability to care for themselves."

"It appears," Hackett said solemnly, "that Cerberus has found a way to fix that."

TBC

AN: This story premise just would not leave my brain. So, no promises on continuation, but I at the very least wanted to get out this first chapter.

Quick rundown, though, for those who are interested in the (game) history:

Spacer/Ruthless/Femshep/Adept

Romanced (kinda) Kaiden in ME1.

Saved Ashley and Kirrahe in ME1.

Romanced (fully) Garrus in ME2.

Mordin died in Collector Base, however Maelon's data saved.

Rachni queen Saved.

Council Saved.

Quarian-Geth peace.

Default Shep Appearance/Name.

Synthesis.


	2. Til She Trembled Thru and Thru

"Confirmation. We've successfully gone through the relay, all ships reporting in."

"All systems are green. We are running silent."

"Colonel, Lieutenant-Colonel Kien for you on the secondary QEC."

The aforementioned Colonel, garbed in a variant of what was standard for N7 Furys yet painted in Cerberus colors, stood up silently and turned towards the door on the left, a short "Captain O'Reily, the bridge is yours" the only acknowledgement of the subordinates' actions.

"Kien," said the Colonel in an almost quiet voice, "is there a reason you are risking your cover in the Major's organization to try and get in contact with me?"

The Lieutenant-Colonel, dressed as he was in the Cerberus variant of an N7 Slayer's armor, shook his head. "I broke off with them in order to bring in a surprising new solution they've engineered in response to our mutual Phantom problem."

"They've found a cure?" mused the Colonel. "How would you rate the effectiveness?"

"Leaving out the amnesia that was a byproduct of our experiment the day after the Crucible firing? It would be like comparing a Cain to a hunting knife, sir."

"Then bring it in, Lieutenant-Colonel. I want a treatment and re-education center for our Phantom's up and running in three weeks."

The blue-ish form of the subordinate saluted the Colonel, "Acknowledged."

"So," the Colonel said while walking up the stairs to the commanding officer's private quarters, "you've managed to get some impressive technology while hiding your operation from both myself and the Alliance. Barring a couple of spies and incidents, I'd say you're doing better than I possibly could have expected, Major. It still remains to be seen, however, if you will ultimately prove successful."

* * *

"Lieutenant Harper," spoke a calm, yet commanding voice on the shuttle's comm speaker, "the facility we're dropping you into is a former research facility of Cerberus, more specifically the Vulcan Station which once powered the entire complex. Your squad's mission is to find and rescue the ex-Cerberus scientists who are being pinned down by a Quarian mercenary group calling themselves the 'Silent Dawn'."

"Quarians, Major?" asked First Lieutenant Harper, her Phantom armor glinting even in the muted light of the shuttle she was in. "What would they want with human scientists?"

"I don't know, Lieutenant, but the Silent Dawn's got a nasty reputation, buried though it is. They've been causing trouble for both above-board and clandestine agencies for the past few months, striking hard, fast, and frequent. They tend to go after experimental technologies, particularly in robotics. If I were to guess, I would say they're trying to covertly discover a way to subjugate the geth."

"I can understand why they would want to keep what they're doing hush-hush, then. No one on Rannoch, Quarian or Geth, wants a second coming of the Morning War. If their motives were to be discovered, no place, in Council or Quarian-Geth space, would be safe for them to hide."

"Exactly," replied the Major, "which is why one of your secondary objectives is to capture one of them alive, if you can. However, I cannot stress this enough that the safe recovery of those scientists takes top priority."

"Understood, sir," said Harper with nod.

"Good," her superior replied, "Smith out."

* * *

_"So, tell me doc, how bad is it?" asked the recently awoken Phantom to the somewhat elderly male in front of her._

_"Jesus," the doctor muttered, before shaking his head to clear his thoughts. "While your eyes have reverted to the acceptable human aesthetic, the majority of your face is so far Reaper-ized that it's impossible to get an identification."_

_This made the Phantom curious, "What about DNA? Shouldn't that work?"_

_The doctor shook his head in the negative. "Ever since the Synthesis Event, all of our DNA records have been rendered useless due to our new genetic makeup."_

_"Synthesis Event? What's that?"_

_"That," said another voice as an older looking man stepped into the room, his Cerberus dress uniform a bright spot against the dark color of the med-bay, "is what we here at Orthrus have been referring to the Crucible firing, and the 3-day event that crippled and removed indoctrination from all Cerberus operatives who had been implanted with Reaper tech."_

_"Orthrus...Wasn't that Cerberus' brother?" asked the Phantom._

_"Indeed. I chose that name for two reasons: To distance ourselves from Cerberus and its actions..."_

_"While at the same time tying yourself to Cerberus, as you have no intention of denying your former allegiance to that organization," the Phantom finished._

_"Exactly," the man replied, "Most of us joined because we felt the Alliance and the Council weren't capable of getting the job done. Just looking at the Collector attacks, and a Cerberus-run operation taking them out once and for all, was enough for many of us to be open to recruitment. That's what this organization is for; to be what Cerberus was meant to be. Not a terrorist organization that lords humanities interests over the rest of the galaxy, but a sword and spear that will protect humanity from the crazies like the ones we were indoctrinated into becoming." He paused a moment, before offering a hand to the Phantom, "I'm Major Adam Smith, and I'd be glad to have your support."_

_"Can you fix my face? Don't think I'm gonna be picking up many dates with a husk's definition of a beautiful face."_

_The Major laughed, "The process takes some time, but yeah, we can work on getting both your face, and if you'll let us, your memories all fixed up."_

_The Phantom shook his hand with a grin._

_The doctor shuddered slightly at the sight. _

* * *

"Quarians, Lieutenant?" asked Jenkins with a somewhat incredulous tone, "We're going up against a shady merc band filled with Quarians?" His arms lay atop his knees as he leaned forward slightly to look at his commanding officer as she walked back from the cockpit.

"What's the matter, Komodo?" asked Nikolic while she leaned back, her rifle lazily held close by one arm. "Got a dextro-based waifu and genetic impossibilities waiting for you at home?"

"Do I detect a note of jealousy, Nikolic?" he quipped back.

"If you're so brain-damaged you're confusing that with good-natured teasing, then yeah, you are indeed, Batman."

Roberts, sitting in the spot next to Nikolic with his turret in his lap, dropped his two cents into the conversation while tinkering with his portable turret. "I heard they rebooted the continuity again."

"What, really?" asked Jenkins as he looked at the other man. "Why would they do that? They've kept the same continuity since before the First Contact War."

"Oi, nerdologists, let's get back into focus, 'kay?" said Nikolic with a shake of her head and shared glance with her commander that basically said _"*sigh*Men...""ugh...I know.." _in the span of a moment.

"You think it's weird for there to be a Quarian mercenary group, Jenkins?" asked Harper as she grabbed one of the support railings on the ceiling of the main cabin of the transport.

"A little bit, yeah," he replied while checking his weapon one last time, "usually Eclipse is the only place merc-inclined quarians go. But then again, with all the weird stuff during and since the Reaper War, I guess it's not too surprising."

"Good point," Harper replied, before twisting the release on the shuttle's door. "Let's move, people! We've got some former colleagues to save, and not a lot of time. I want none of you dead, and our enemy blown to tiny bits. Am I clear?"

"Hooah, LT!" came the reply from three different throats.

* * *

"Liara, mind telling me what this is about?" asked Garrus Vakarian as he took a seat across from the Shadow Broker at a Presidium Cafe.

"I think I may have tracked down who absconded with their remains, Garrus," was all Liara said before sliding a datapad in the turians direction.

"Their?" he asked, his subharmonics barely betraying his sudden trepidation.

"Admiral Anderson, and..."

_Jane Shepard..._ was the unspoken thought they both shared.

His hands twitched. He wanted a gun in his hand. And lots of enemies to shoot along with it. "Who was it?"

"Cerberus," said Liara. And Garrus's expression of incredulity, she explained further, "It appears that several remnants of Cerberus still operate with relative impunity, even months after the war's end. Some, like the splinter group Orthrus, are actually relatively helpful towards galactic security, even if they operate outside the bounds of Alliance jurisdiction. The largest remnant, however, is a combination of an entire Cerberus battle group and one of its last remaining loyal science cells. They are run by a Colonel Connie West, a ruthless biotic who was in charge of Project Phantom."

"Oh good. I always wondered whose ass needed kicking in response to those crazy," he paused and glanced at Liara, "what did Ash call them? 'Ninja' girls?"

"Speaking of Ash, would you mind working with her and the Normandy again, for one last mission?"

"What do you mean?" asked Garrus.

"We know for sure that they took Anderson's body. But, if there's even a chance that they have _hers_..."

"Don't worry Liara, I think it's worth it too. Shepard deserves the rest."

TBC

AN: Not very action-y this chapter, I know, but plot does have its place in the grand scheme of things. Trying to keep OC's to a relative minimum, while having a story almost entirely focused on them post Synthesis-ending, is a fun yet exciting challenge.


End file.
